Since the i2c is not available, what is the best way to connect additional rangefinders such as sonars and lidars to the Aero board?

I plan to connect the Aero with the Pixhawk in the future instead of the RTF flight controller. I see that the tutorials use UART to do so. In such a setup, is the 80pin breakout ports no longer functional? Is there any drawbacks when accessing flight controller data that we should be aware of?

With the Intel Aero Compute Board, you can connect the Pixhawk flight controller via HSUART and using the FPGA to configure serval interfaces like I2C, PWMs, ADC, and GPIO. You can use the 80 pin IO expansion connector to expose the interfaces but would require you to configure the FPGA. You may need to design your own expansion cable/board if the 80 pin IO expansion connector does not meet your requirements.

There has been a complication with this solution. I recently read in several forums that for PX4 and APM platforms, the flight controller needs to be in "offboard" or "Guided_nogps" flight modes, which turns off any pixhawk's sensor fusion based functionalities such as Altitude Hold.

My architecture relies on the pixhawk to fly in Altitude Hold mode to simplify my navigation algorithms to a 2D problem. Is there a way around this flight mode restriction? For example, could I somehow convert the mavros Attitude commands into PPM signals and output it through HSUART and directly to the PPM input pins on the pixhawk?

I have not explored this area myself and can only make some suggestions. Have you tried sending setpoints with the same altitude? I'm not sure if this will meet your project requirements. Take a look at Ardupilot, they have offboard with GPS data. http://ardupilot.org/dev/docs/companion-computers.html

Regarding the PPM signals, I'm not sure if this would be possible as I have not done this myself.